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A position-dependent stochastic diffusion model of gating in ion channels is developed by considering the spatial variation of the diffusion coefficient between the closed and open states. It is assumed that a sensor which regulates the…
Motivated by the diffusion-reaction kinetics on interstellar dust grains, we study a first-passage problem of mortal random walkers in a confined two-dimensional geometry. We provide an exact expression for the encounter probability of two…
We describe a universal transition mechanism characterizing the passage to an annealed behavior and to a regime where the fluctuations about this behavior are Gaussian, for the long time asymptotics of the empirical average of the expected…
We study diffusive mixing in the presence of thermal fluctuations under the assumption of large Schmidt number. In this regime we obtain a limiting equation that contains a diffusive thermal drift term with diffusion coefficient obeying a…
We consider the trapping reaction, $A+B\to B$, where $A$ and $B$ particles have a diffusive dynamics characterized by diffusion constants $D_A$ and $D_B$. The interaction with $B$ particles can be formally incorporated in an effective…
Prompted by results that showed that a simple protein model, the frustrated G\=o model, appears to exhibit a transition reminiscent of the protein dynamical transition, we examine the validity of this model to describe the low-temperature…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is…
A wide range of quasi-one-dimensional materials, consisting of weakly coupled chains, undergo three-dimensional phase transitions that can be described by a complex order parameter. A Ginzburg-Landau theory is derived for such a transition.…
The problem of escape of a Brownian particle in a cusp-shaped metastable potential is of special importance in nonadiabatic and weakly-adiabatic rate theory for electron transfer (ET) reactions. Especially, for the weakly-adiabatic…
We compute the temperature-dependent barrier for alpha-relaxations in several liquids, without adjustable parameters, using experimentally determined elastic, structural, and calorimetric data. We employ the random first order…
This work investigates one- and two-neutron transfer in the $^{96}\text{Zr} + {}^{40}\text{Ca}$ reaction at sub-barrier energies using a microscopic framework based on time-dependent covariant density functional theory (TD-CDFT). Pairing…
The self-diffusion process of a hard sphere fluid confined by two parallel plates separated by a distance on the order of the particle diameter is studied. The starting point is a closed kinetic equation for the distribution function that…
We investigate by Montecarlo simulation the linear response function of three dimensional structural glass models defined by short-range kinetic constraints and a trivial equilibrium Boltzmann-Gibbs measure. The breakdown of the…
Many processes in chemistry, physics, and biology depend on thermally activated events in which the system changes its state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation…
We investigate a one-dimensional water-like lattice model with Van der Waals and hydrogen-bond interactions, allowing for particle number fluctuations through a chemical potential. The model, defined on a chain with periodic boundary…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
In this paper we study the kinetics of diffusion-limited, pseudo-first-order A + B -> B reactions in situations in which the particles' intrinsic reactivities vary randomly in time. That is, we suppose that the particles are bearing "gates"…
Thermally activated phenomena in physics and chemistry, such as conformational changes in biomolecules, liquid film rupture, or ferromagnetic field reversal, are often associated with exponentially long transition times described by…
In this paper we develop an encounter-based model of reaction-subdiffusion in a domain $\Omega$ with a partially absorbing interior trap $\calU\subset \Omega$. We assume that the particle can freely enter and exit $\calU$, but is only…